I know you're looking for rules, but I would make an arguement against such counters "instant death". My thought is that having monsters and spells with such abilities forces a party to be prepared. If your cleric/wizard are using 100% of their prepared spells for offensive/buffing, then why should they be rewarded for not preparing their spell lists carefully? Having such effects such as petrification, disintigration, death effects, negative energy and so forth are a part of the experience and monsters that have such capabilities are, for the most part, balanced in CR against parties that should have the capabilities to respond to such threats. If your wizard doesn't keep a Stone to Flesh scroll handy, or your cleric doesn't keep a Revivify or Restoration handy, then again I would say they should not be rewarded with an out to bypass or hamstring such rules.
If they learn the hard way, so be it. I have spent more than my fair share of sitting back and watching the combat after my character has died (I am the clear leader in character deaths, dismemberments and incapacitations in my group) and I have no problem with it. Nine times out of ten it's the direct result of my actions. It's part of the game and part of the fun.
Now, if you have a small group, with 2 or 3 PCs, or if the DM is throwing such creatures against a party that isn't high enough level to be able to handle them, then I can see a need for such rules, even if they are house rules. But for normal game play, again I would argue against. Let them learn the hard way to work as a team and to be prepared, if that's what it takes.
I also believe that such rules to alter the "instant death" effects of these spells and monsters will alter the balance and challenge these foes would normally present. So if you allow other rules to bypass or weaken it, then I would counter that you must also lower the CR that these foes have. For your example, the CR7 medusa, would become a CR4. I would even make her a CR3 as a medusa with a severly hampered/weakened gaze attack is not that challenging a foe. If they're not facing the fully strength foe, they shouldn't get the full xp reward.
That's my view of it as someone who is usually player and occasionally DM.